"Hágase" is an imperative and "que se haga" is closer to making a wish.
In most religious environments I've seen, the imperative is more common when it's a priest who speaks, while the "wish" form is more often heard when it's someone else who's praying.

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As a quick but rather limited corpus experiment, translations of Matthew 6:10 (part of the Lord's prayer / Padrenuestro) seem to use predominantly hágase, followed by sea hecha. Exact proportions depend on how much weight you want to give to the various editions of the Reina Valera.